Microarray-based analysis of the BRAF V600 mutations in circulating tumor DNA in melanoma patients

Background: Circulating tumor DNA (ctDNA) holds great potential for cancer therapy and can provide diagnostic and prognostic information before and during treatment. Methods: Plasma DNA samples from 97 melanoma patients, 20 healthy donors and 3 patients with benign skin tumors were analyzed by microarray analysis and droplet digital PCR (ddPCR). Results: A microarray for simultaneous detection of six BRAF V600 mutations in ctDNA has been developed. The method allows the detection of 0.05% mutated DNA from WT DNA background. For paired samples (pre-surgery plasma and tumor tissue) isolated from 74 patients, the concordance of genotypes between tumor DNA and ctDNA was 65% (48/74). BRAF mutations in ctDNA were detected in 27/50 patients with BRAF-positive tumors and in 3/24 patients with BRAF wild-type tumors. The presence of ctDNA BRAF mutations in 23 plasma samples from melanoma patients undergoing therapy correlated significantly with tumor progression (P=0.005). The increase in cell-free DNA levels measured by ddPCR also correlated with disease progression (P=0.02). The concordance of results obtained by microarray identification of BRAF mutations and those obtained by ddPCR was 91%. Conclusion: The novel microarray-based approach can be a useful non-invasive tool for accurate identification of ctDNA BRAF mutations to monitor disease progression. (C) 2020 Elsevier Inc. All rights reserved.

Automated summary

This study developed a novel microarray technology for simultaneous detection of six BRAF V600 mutations in ctDNA, and showed high concordance in genotypes between ctDNA and tumor tissue DNA for evaluating disease progression in melanoma patients. The novel microarray-based approach demonstrated high accuracy in monitoring disease progression of melanoma patients by detecting ctDNA BRAF mutations.